The problem hasn't been solved
Hi,
Hi,
I have been trying to perform Ligand Docking with the ROSETTA software. I describe what I have done:
1. First, I have the ligands in sdf/mol2 format one per file. I add hydrogens to these and create the params files with the "molfile_to_params.py" script.
2. Second, I clean the protein (no ligands or cofactors) and add H to the protein.
3. Third, I concatenate the protein with each ligand in a different file for each ligand (the ligand has chain identifier X, the protein A).
Hi,
I want to perform LigandDocking with ROSIE, but I have many ligands and it is not possible to run each one from the webserver. Is there a way to run ROSIE from the terminal/command line?
Thank you
I am facing SEGMENTATION FAULT error when I try to generate 10000 structures in Rosetta Homology modelling. I am running this through the Batch script. For example, when I give -out:nstruct 10000 in the flag file, it generates only 48 structures after that the job gets terminated. I have attached my batch script, flag file, Error file and the Rosettta_crash.log file here. Please, can anyone help me to find the solution to this problem?
Flag File
Hi Rosetta Team!
I read from the scoring tutorial this line
A rule of thumb: -1 to -3 REU per residue is typical while scoring a refined structure with ref2015 score function.
May I know if it is possible to directly call this per residue total score during scoring?
Thank you.
I have been attempting to apply dihedral constraints to the phi/psi angles of a small TRP dipeptide minimization without success. From the output pdb it appears the second dihedral constraint is not applied to the CN atom of the Acetylayted end cap. This dihedral angle shifts to 150 degrees despite a very strong constraint. I suspect Rosetta might be selecting the first CN atom it finds which would be the methyl carbon on the NME cap rather than the carbonyl carbon on the ACE group of the same name.
Hello everyone,
I recently read in the manual that "partners" parameter must be set in the order of how they are set in the PDB. However, I was unaware of this previously and set my partners as LH_A, while my pdb files are ordered as HLA. The docking is working and has been running for a couple days, but I am wondering if this will affect the results of the docking?
My GitHub account does not have verified academic email address, while my institution is academic.
My institution is Isfahan University of Medical Sciences
My academic Email is h.aria256@resident.mui.ac.ir
After I had moved to the input_file directory following the Controlling Input and Output in Rosetta,I ran,
$ROSETTA3/bin/score_jd2.default.linuxgccrelease -in:file:s input_files/1qys.pdb
and I got the output,
-bash: /bin/score_jd2.default.linuxgccrelease: No such file or directory.
What would you recommend doing?
